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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PDXY PROTEIN FROM ESCHERICHIA COLI
 
Authors :  M. K. Safo, F. N. Musayev, S. Hunt, M. Di Salvo, N. Scarsdale, V. Schirch
Date :  21 May 04  (Deposition) - 13 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pyridoxal Kinase, Ribokinase Family, Kinase, Phosphorylation, Pdxy, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. K. Safo, F. N. Musayev, S. Hunt, M. L. Di Salvo, N. Scarsdale, V. Schirch
Crystal Structure Of The Pdxy Protein From Escherichia Coli
J. Bacteriol. V. 186 8074 2004
PubMed-ID: 15547280  |  Reference-DOI: 10.1128/JB.186.23.8074-8082.2004
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYRIDOXAMINE KINASE
    Chains: A, B
    EC Number: 2.7.1.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 22
    Expression System Strain: HMS 174(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PDXY, B1636
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: PM KINASE, PDXY PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1PXL2Ligand/Ion3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE
2SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:221 , VAL B:222 , GLY B:223 , ASP B:224 , PXL B:289 , HOH B:538 , HOH B:553BINDING SITE FOR RESIDUE SO4 B 288
2AC2SOFTWARESER A:10 , HIS A:44 , THR A:45 , GLN A:46 , TYR A:83 , CYS A:122 , VAL A:220 , ASP A:224BINDING SITE FOR RESIDUE PXL A 288
3AC3SOFTWARESER B:10 , HIS B:44 , THR B:45 , TYR B:83 , CYS B:122 , VAL B:220 , ASP B:224 , SO4 B:288BINDING SITE FOR RESIDUE PXL B 289

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TD2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TD2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TD2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1TD2)

(-) Exons   (0, 0)

(no "Exon" information available for 1TD2)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:287
 aligned with PDXY_ECOLI | P77150 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:287
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       
           PDXY_ECOLI     1 MMKNILAIQSHVVYGHAGNSAAEFPMRRLGANVWPLNTVQFSNHTQYGKWTGCVMPPSHLTEIVQGIAAIDKLHTCDAVLSGYLGSAEQGEHILGIVRQVKAANPQAKYFCDPVMGHPEKGCIVAPGVAEFHVRHGLPASDIIAPNLVELEILCEHAVNNVEEAVLAARELIAQGPQIVLVKHLARAGYSRDRFEMLLVTADEAWHISRPLVDFGMRQPVGVGDVTSGLLLVKLLQGATLQEALEHVTAAVYEIMVTTKAMQEYELQVVAAQDRIAKPEHYFSATKL 287
               SCOP domains d1td2a_ A: Pyridoxamine kinase                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1td2A00 A:1-287  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.....hhhhhhhhhhhh..eeeeeeeeee..hhhhh...eee.hhhhhhhhhhhhhhh.hhhhh.eeee....hhhhhhhhhhhhhhhhhhh...eeee...............hhhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhh....eeee..hhhhh....eeeeeee....eeeeeee..........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhh.......ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1td2 A   1 MMKNILAIQSHVVYGHAGNSAAEFPMRRLGANVWPLNTVQFSNHTQYGKWTGCVMPPSHLTEIVQGIAAIDKLHTCDAVLSGYLGSAEQGEHILGIVRQVKAANPQAKYFCDPVMGHPEKGCIVAPGVAEFHVRHGLPASDIIAPNLVELEILCEHAVNNVEEAVLAARELIAQGPQIVLVKHLARAGYSRDRFEMLLVTADEAWHISRPLVDFGMRQPVGVGDVTSGLLLVKLLQGATLQEALEHVTAAVYEIMVTTKAMQEYELQVVAAQDRIAKPEHYFSATKL 287
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       


Chain B from PDB  Type:PROTEIN  Length:287
 aligned with PDXY_ECOLI | P77150 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:287
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       
           PDXY_ECOLI     1 MMKNILAIQSHVVYGHAGNSAAEFPMRRLGANVWPLNTVQFSNHTQYGKWTGCVMPPSHLTEIVQGIAAIDKLHTCDAVLSGYLGSAEQGEHILGIVRQVKAANPQAKYFCDPVMGHPEKGCIVAPGVAEFHVRHGLPASDIIAPNLVELEILCEHAVNNVEEAVLAARELIAQGPQIVLVKHLARAGYSRDRFEMLLVTADEAWHISRPLVDFGMRQPVGVGDVTSGLLLVKLLQGATLQEALEHVTAAVYEIMVTTKAMQEYELQVVAAQDRIAKPEHYFSATKL 287
               SCOP domains d1td2b_ B: Pyridoxamine kinase                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1td2B00 B:1-287  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                                           CATH domains
           Pfam domains (1) --------------------------------------------------Phos_pyr_kin-1td2B01 B:51-268                                                                                                                                                                                             ------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------Phos_pyr_kin-1td2B02 B:51-268                                                                                                                                                                                             ------------------- Pfam domains (2)
         Sec.struct. author ...eeeeee........hhhhhhhhhhhh..eeeeee.eee..hhhhh...eee.hhhhhhhhhhhhhhh.hhhhh.eeee....hhhhhhhhhhhhhhhhhhh...eeee...............hhhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhhh...eeee..hhhhh.....eeeeee....eeeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhh.......ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1td2 B   1 MMKNILAIQSHVVYGHAGNSAAEFPMRRLGANVWPLNTVQFSNHTQYGKWTGCVMPPSHLTEIVQGIAAIDKLHTCDAVLSGYLGSAEQGEHILGIVRQVKAANPQAKYFCDPVMGHPEKGCIVAPGVAEFHVRHGLPASDIIAPNLVELEILCEHAVNNVEEAVLAARELIAQGPQIVLVKHLARAGYSRDRFEMLLVTADEAWHISRPLVDFGMRQPVGVGDVTSGLLLVKLLQGATLQEALEHVTAAVYEIMVTTKAMQEYELQVVAAQDRIAKPEHYFSATKL 287
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Ribokinase (55)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PDXY_ECOLI | P77150)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0008478    pyridoxal kinase activity    Catalysis of the reaction: ATP + pyridoxal = ADP + pyridoxal 5'-phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0009443    pyridoxal 5'-phosphate salvage    Any process that generates pyridoxal 5'-phosphate, the active form of vitamin B6, from derivatives of it without de novo synthesis.
    GO:0042817    pyridoxal metabolic process    The chemical reactions and pathways involving 3-hydroxy-5-(hydroxymethyl)-2-methyl-4-pyridinecarboxaldehyde, one of the vitamin B6 compounds. Pyridoxal, pyridoxamine and pyridoxine are collectively known as vitamin B6, and are efficiently converted to the biologically active form of vitamin B6, pyridoxal phosphate.
    GO:0042819    vitamin B6 biosynthetic process    The chemical reactions and pathways resulting in the formation of any of the vitamin B6 compounds; pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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        PDXY_ECOLI | P77150: 1vi9

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